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mitoNGS / MToolBox

A bioinformatics pipeline to analyze mtDNA from NGS data
http://sourceforge.net/projects/mtoolbox/?source=navbar
GNU General Public License v3.0
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line 207: `in-out_folders': not a valid identifier #16

Closed bobbieshaban closed 8 years ago

bobbieshaban commented 8 years ago

Hi,

I am trying to run MToolbox and I am receiving the error "line 207: `in-out_folders': not a valid identifier"

I performed a standard installation and this is my config shell [shabanb@thing1 mtoolsbox]$ cat config_me.sh input_type=fastq ref=CG5.target output_name=/data/Bioinfo/bioinfo-proj-bobbie/newProgs/MtoolBox/CAGRF10964/mtoolsbox/test_out/

my file names are as such CG5_ALE07.R1.fastq CG5_ALE07.R2.fastq CG5.target.fa

And below is the full command and output `[shabanb@thing1 mtoolsbox]$ sh MToolBox.sh -i config.sh -m "-t 20" -a "-t 10 -z 0.6"

setting up MToolBox environment variables... ...done

setting up MToolBox variables in config file ... ...done

Check python version... (2.7 required) OK.

Checking files to be used in MToolBox execution...

Checking mapExome parameters... OK.

Checking assembleMTgenome parameters... OK.

Checking mt-classifier parameters... OK. /data/Bioinfo/bioinfo-proj-bobbie/newProgs/MtoolBox/MToolBox/MToolBox.sh: line 207: in-out_folders': not a valid identifier

bobbieshaban commented 8 years ago

Sorry, the command line is actually

sh MToolBox.sh -i config_me.sh -m "-t 20" -a "-t 10 -z 0.6"

which produces the same error.

Thanks for your help!

domenico-simone commented 8 years ago

Hi Bobby,

sorry for this huge delay in replying. Apparently there could be some issue in the name we adopted for the function, even if it's the first time we have a report like this. Which OS do you use?

Best regards, Domenico

domenico-simone commented 8 years ago

I have changed the name of the function in-out_folder in in_out_folder which should be more compliant to a wider range of standards.

bobbieshaban commented 8 years ago

Thanks Domenico!

I will download again and give another test.

Bobbie.

From: Domenico Simone [mailto:notifications@github.com] Sent: Wednesday, 5 October 2016 9:44 AM To: mitoNGS/MToolBox Cc: Bobbie Shaban; Author Subject: Re: [mitoNGS/MToolBox] line 207: `in-out_folders': not a valid identifier (#16)

I have changed the name of the function in-out_folder in in_out_folder which should be more compliant to a wider range of standards.

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